Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Errors and warnings explanation #416

Open
zhangkn3 opened this issue Mar 8, 2024 · 2 comments
Open

Errors and warnings explanation #416

zhangkn3 opened this issue Mar 8, 2024 · 2 comments

Comments

@zhangkn3
Copy link

zhangkn3 commented Mar 8, 2024

Hi Andre,
Hope everything goes well with you!
I have been using Bambu for months. It is a really good one.
However, I met these errors and warnings these days, and the job seems to be halted. But even with these errors and warnings, I can still get the results and novel transcripts from Bambu. Do I need to do something to solve the issues, or I can just ignore them?
Here are my codes when running Bambu.

library(bambu)
gencode_seq <- "/gpfs/fs1/data/hg38.fa"
gencode_gtf <- prepareAnnotations("/gpfs/fs1/data/hg38.knownGene.gtf")
uncorrected_bam_file <- "/gpfs/fs1/data/filtered_minimaped_GBM013.sort.bam"
corrected_bam_file <- "/gpfs/fs1/data/filtered_corrected_minimaped_GBM013.sort.bam"
ont_iso_analysis <- bambu(reads = c(uncorrected_bam_file, corrected_bam_file), annotations = gencode_gtf, genome = gencode_seq, ncore = 8)
writeBambuOutput(ont_iso_analysis, path = "/gpfs/fs1/data/GBM013/")
ont_iso_analysis.novel <- ont_iso_analysis[mcols(ont_iso_analysis)$novelTranscript,]
writeBambuOutput(ont_iso_analysis.novel, path = "/gpfs/fs1/data/GBM013/novel/")

And, these are the issue reports.
image

Looking forward to your response!
Best,
Kenan
@andredsim
Copy link
Collaborator

Hi Kenan,

If you are meaning the xgboost warnings, that is fine to ignore. We just need to update the packages and push the changes. We just keep getting distracted with other tasks but I will hopefully find the time to do this soon.
Given that bambu() finishes running, and the remaining warnings are not result impacting I think its fine to ignore for now. I believe the finally warnings must be happening during the writeBambuOutput() function call. But as you are still getting your outputs I think that should be fine too.

Do you still get the error: subscript contains invalid names
If you do not run this line
ont_iso_analysis.novel <- ont_iso_analysis[mcols(ont_iso_analysis)$novelTranscript,]
and instead output the whole analysis?
writeBambuOutput(ont_iso_analysis, path = "/gpfs/fs1/data/GBM013/novel/")
I am wondering if perhaps the filtering is doing something we didn't forsee.

Best of luck with your future runs of Bambu

Kind Regards,
Andre Sim

@zhangkn3
Copy link
Author

Thanks Andre,
I will run the code and come to you later.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@andredsim @zhangkn3